QIIME and Pielou inxdex (alpha diversity)

[veb...@plantgene.eu]

Hi all,

I was interested to calculate the Pielou index for my alpha diversity (skbio.diversity.alpha.pielou_e) unfortunately I see that QIIME is using old version of scikit-bio (only for python 2 ) where this index is missing. This index is present in the new scikit-bio packages which are only for pythin3 and I was wondering is there a way to get these values from alpha_diversity.py?

Thanks!

[Daniel McDonald]

Hello,

Unfortunately, I don't see a means to get it via alpha_diversity.py in QIIME 1.9.x. Are you familiar with Python scripting? It probably is only a few lines of code. If not, I'd be happy to provide a script which can use scikit-bio 0.5.0 to generate this index. As you note though, scikit-bio no longer supports Python 2, so there will need to be a little environment management to do this. Please let me know how you'd like to proceed.

Best,

Daniel

[veb...@plantgene.eu]

Dear Daniel,

I will be happy if you can provide me with a script to generate the index, many thanks!

Vesko

[Daniel McDonald]

Hi Vesko,

Please find the script attached. It can be used with:

$ python pielou_e.py <your_biom_table> <name_of_output_file>

The script requires Python 3, BIOM-Format >= 2.1.5 and scikit-bio >= 0.5.0. If you've got conda, this environment can be created with:

$ conda create --name pielou_e -c bioconda python=3 biom-format scikit-bio

Best,

Daniel 

[veb...@plantgene.eu]

Many thanks, this worked like charm :)

[Daniel McDonald]

Great!